The dissection of the circadian clock into its molecular
components represents the most striking and well-studied
example of a gene regulatory network underlying a
complex behavioural trait. By contrast, the evolutionary
analysis of the clock has developed more slowly. Here
we review studies that have surveyed intraspecific clock
gene variation over large geographical areas and have
discovered latitudinal clines in gene frequencies. Such
spatial patterns traditionally suggest that natural selection
shapes genetic variation, but it is equally possible
that population history, or a mixture of demography and
selection, could contribute to the clines. We discuss how
population genetics, together with functional assays,
can illuminate these possible cases of natural selection
in Drosophila clock genes.